Tsukihara S, Akiyama Y, Shimada S, Hatano M, Igarashi Y, Taniai T, Tanji Y, Kodera K, Yasukawa K, Umeura K, Kamachi A, Nara A, Okuno K, Tokunaga M, Katoh H, Ishikawa S, Ikegami T, Kinugasa Y, Eto K, Tanaka S. Delactylase effects of SIRT1 on a positive feedback loop involving the H19-glycolysis-histone lactylation in gastric cancer. Oncogene 2024 Dec 11.
Ding, T., Wagner, S.J., Song, A.H., Chen, R.J., Lu, M.Y., Zhang, A., Vaidya, A.J., Jaume, G., Shaban, M., Kim, A., Williamson, D.F.K., Chen, B., Almagro-Perez, C., Doucet, P., Sahai, S., Chen, C., Komura, D., Kawabe, A., Ishikawa, S., Gerber, G., Peng, T., Le, L.P., Mahmood, F., Multimodal Whole Slide Foundation Model for Pathology. arXiv 2024 2411.19666
Yang, C., Komura, D., Kakiuchi, M., Ochi M., Katoh H., Ushiku, T., Ishikawa S., SegRep: Mask-Supervised Learning for Segment Representation in Pathology Images. IEEE Access 2024 12: 141729
Torazawa S, Miyawaki S, Imai H, Hongo H, Ishigami D, Shimizu M, Sakai Y, Ogawa S, Kiyofuji S, Koizumi S, Komura D, Katoh H, Ono H, Nakatomi H, Ishikawa S, Saito N. Association of rare variants in RNF213 with severe progression of intracranial artery stenosis in quasi-moyamoya disease. J Neurosurg. 2024 Sep 13:1-10.
Taki T, Koike Y, Adachi M, Sakashita S, Sakamoto N, Kojima M, Aokage K, Ishikawa S, Tsuboi M, Ishii G. A novel histopathological feature of spatial tumor-stroma distribution predicts lung squamous cell carcinoma prognosis. Cancer Sci. 2024 Sep 3.
Adachi M, Taki T, Kojima M, Sakamoto N, Matsuura K, Hayashi R, Tabuchi K, Ishikawa S, Ishii G, Sakashita S. Predicting lymph node recurrence in cT1-2N0 tongue squamous cell carcinoma: collaboration between artificial intelligence and pathologists. J Pathol Clin Res. 2024 Sep;10(5):e12392.
Hirano Y, Miyawaki S, Sakai Y, Teranishi Y, Okano A, Umekawa M, Hongo H, Torazawa S, Ogawa S, Komura D, Katoh H, Ikemura M, Ushiku T, Ishikawa S, Saito N. Genetic analysis of foramen magnum meningiomas reveals AKT1 mutations uncomplicated by TRAF7 mutations. Acta Neuropathol Commun. 2024 Aug 5;12(1):123.
Ochi M, Komura D, Ishikawa S. Pathology Foundation Models. arXiv 2024 2407.21317
Ito S, Matsunaga R, Nakakido M, Komura D, Katoh H, Ishikawa S, Tsumoto K. High-throughput system for the thermostability analysis of proteins. Protein Sci. 2024 Jun;33(6):e5029.
Herdiantoputri RR, Komura D, Ochi M, Fukawa Y, Kayamori K, Tsuchiya M, Kikuchi Y, Ushiku T, Ikeda T, Ishikawa S. Benchmarking Deep Learning-Based Image Retrieval of Oral Tumor Histology. Cureus. 2024 Jun 12;16(6):e62264.
Yang, C., Komura, D., Kakiuchi, M., Ochi M., Katoh H., Ushiku, T., Ishikawa S., SegRep: Mask-Based Self-Supervised Learning for Segment Representation in Pathology Images. TechRxiv February 12, 2024.
Ochi M, Komura D, Onoyama T, Shinbo K, Endo H, Odaka H, Kakiuchi M, Katoh H, Ushiku T, Ishikawa S. Registered multi-device/staining histology image dataset for domain-agnostic machine learning models. Scientific Data 2024 Apr 3;11(1):330.
Torazawa S, Miyawaki S, Imai H, Hongo H, Ono H, Ogawa S, Sakai Y, Kiyofuji S, Koizumi S, Komura D, Katoh H, Ishikawa S, Saito N. Association of Genetic Variants with Postoperative Donor Artery Development in Moyamoya Disease: RNF213 and Other Moyamoya Angiopathy-Related Gene Analysis. Translational Stroke Research 2024 Apr 9.
Nagasaki Y, Taki T, Nomura K, Tane K, Miyoshi T, Samejima J, Aokage K, Ohtani-Kim SJ, Kojima M, Sakashita S, Sakamoto N, Ishikawa S, Suzuki K, Tsuboi M, Ishii G. Spatial intratumor heterogeneity of programmed death-ligand 1 expression predicts poor prognosis in resected non-small cell lung cancer. J Natl Cancer Inst. 2024 Mar 8:djae053.
Ishikawa S. Artificial Intelligence Enhances NSCLC Care by Predicting Treatment Outcomes, Validating Neoadjuvant Therapies, and Improving Precision. J Thorac Oncol. 2024 May;19(5):666-667.
Kawai H, Miura T, Kawamatsu N, Nakagawa T, Shiba-Ishii A, Yoshimoto T, Amano Y, Kihara A, Sakuma Y, Fujita K, Shibano T, Ishikawa S, Ushiku T, Fukayama M, Tsubochi H, Endo S, Hagiwara K, Matsubara D, Niki T. Expression patterns of HNF4α, TTF-1, and SMARCA4 in lung adenocarcinomas: impacts on clinicopathological and genetic features. Virchows Arch. 2024 May 6.
Matsuno, A., Sumida, H., Nakanishi, H., Ikeyama, Y., Ishii, T., Omori, I., Matsuno A, Sumida H, Nakanishi H, Ikeyama Y, Ishii T, Omori I, Saito H, Iwasawa O, Sugimori A, Yoshizaki A, Katoh H, Ishikawa S, Sato S. Keratinocyte proline-rich protein modulates immune and epidermal response in imiquimod-induced psoriatic skin inflammation. Exp Dermatol. 2023.
Akiyama Y, Harada K, Miyakawa J, Kreder KJ, O’Donnell MA, Daichi M, Katoh H, Hori M, Owari K, Futami K, Ishikawa S, Ushiku T, Kume H, Homma Y, Luo Y. Th1/17 polarization and potential treatment by an anti-interferon-γ DNA aptamer in Hunner-type interstitial cystitis. iScience 2023:108262.
Tsubosaka A, Komura D, Kakiuchi M, Katoh H, Onoyama T, Yamamoto A, Abe H, Seto Y, Ushiku T, Ishikawa S. Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach. Cell Reports 2023;42:113236.
Teranishi Y, Miyawaki S, Nakatochi M, Okano A, Ohara K, Hongo H, Ishigami D, Sakai Y, Shimada D, Takayanagi S, Ikemura M, Komura D, Katoh H, Mitsui J, Morishita S, Ushiku T, Ishikawa S, Nakatomi H, Saito N. Meningiomas in patients with neurofibromatosis type 2 predominantly comprise “immunogenic subtype” tumours characterised by macrophage infiltration. Acta Neuropathol Commun 2023;11:156.
Sakata J, Tatsumi T, Sugiyama A, Shimizu A, Inagaki Y, Katoh H, Yamashita T, Takahashi K, Aki S, Kaneko Y, Kawamura T, Miura M, Ishii M, Osawa T, Tanaka T, Ishikawa S, Tsukagoshi M, Chansler M, Kodamad T, Kanai M, Tokuyama H, Yamatsugu K. Antibody-mimetic drug conjugate with efficient internalization activity using anti-Her2 VHH and duocarmycin. Protein Expression and Purification 2023:106375.
Morisue, R., Kojima, M., Suzuki, T., Watanabe, R., Sakamoto, N., Sakashita, S., Harada, K., Nakai, T., Ishii, G., Nakatsura, T., Gotohda, N., Ishikawa, S., 2023. Common clinicopathological and immunological features of sarcomatoid carcinoma across organs: A histomorphology-based cross-organ study. Int J Cancer.
Akiyama, Y., Sonehara, K., Maeda, D., Katoh, H., Naito, T., Yamamoto, K., Biobank Japan Project, Morisaki, T., Ishikawa, S., Ushiku, T., Kume, H., Homma, Y., Okada, Y., 2023. Genome-wide association study identifies risk loci within the major histocompatibility complex region for Hunner-type interstitial cystitis. Cell Reports Medicine 4, 101114.
Kojima, M., Yokota, M., Yanagisawa, N., Kitamura, S., Amemiya, K., Kawano, S., Tsukada, Y., Sakuyama, N., Nagayasu, K., Hashimoto, T., Nakashima, K., Jiang, K., Kanemitsu, Y., Fujita, F., Akiba, J., Notohara, K., Itakura, J., Sekine, S., Sakashita, S., Sakamoto, N., Ishikawa, S., Nakanishi, Y., Yao, T., Liang, W.-Y., Lauwers, G.Y., Ito, M., Sakamoto, K., Ishii, G., Ochiai, A., 2023. Assessment of Elastic Laminal Invasion Contributes to an Objective pT3 Subclassification in Colon Cancer. Am J Surg Pathol.
Torazawa, S., Miyawaki, S., Imai, H., Hongo, H., Ishigami, D., Shimizu, M., Ono, H., Shinya, Y., Sato, D., Sakai, Y., Umekawa, M., Kiyofuji, S., Shimada, D., Koizumi, S., Komura, D., Katoh, H., Ishikawa, S., Nakatomi, H., Teraoka, A., Saito, N., 2023. RNF213 p.Arg4810Lys Wild Type is Associated with De Novo Hemorrhage in Asymptomatic Hemispheres with Moyamoya Disease. Transl Stroke Res.
Yukawa, N., Yamada, T., Aoyama, T., Woo, T., Ueda, K., Mastuda, A., Hara, K., Kazama, K., Tamagawa, H., Sato, T., Oshima, T., Suzuki, A., Aburatani, H., Ishikawa, S., Saito, A., Masuda, M., Yoshida, H., Rino, Y., 2023. Tumor DNA in Peritoneal Lavage as a Novel Biomarker for Predicting Peritoneal Recurrence in Patients With Gastric Cancer. Anticancer Res 43, 2069–2076.
Herdiantoputri, R.R., Komura, D., Ikeda, T., Ishikawa, S., 2023. Head and Neck Tumor Histopathological Image Representation with Pre- Trained Convolutional Neural Network and Vision Transformer. J Dent Indones. 30, 41–47.
Herdiantoputri, R.R., Komura, D., Fujisaka, K., Ikeda, T., Ishikawa, S., 2023. Deep texture representation analysis for histopathological images. STAR Protoc 4, 102161.
Totoki, Y., Saito-Adachi, M., Shiraishi, Y., Komura, D., Nakamura, H., Suzuki, A., Tatsuno, K., Rokutan, H., Hama, N., Yamamoto, S., Ono, H., Arai, Y., Hosoda, F., Katoh, H., Chiba, K., Iida, N., Nagae, G., Ueda, H., Shihang, C., Sekine, S., Abe, H., Nomura, S., Matsuura, T., Sakai, E., Ohshima, T., Rino, Y., Yeoh, K.G., So, J., Sanghvi, K., Soong, R., Fukagawa, A., Yachida, S., Kato, M., Seto, Y., Ushiku, T., Nakajima, A., Katai, H., Tan, P., Ishikawa, S., Aburatani, H., Shibata, T., 2023. Multiancestry genomic and transcriptomic analysis of gastric cancer. Nature Genetics 1–14.
Komura, D., Onoyama, T., Shinbo, K., Odaka, H., Hayakawa, M., Ochi, M., Herdiantoputri, R.R., Endo, H., Katoh, H., Ikeda, T., Ushiku, T., Ishikawa, S., 2023. Restaining-based annotation for cancer histology segmentation to overcome annotation-related limitations among pathologists. Patterns 4, 100688.
Katoh, H., Komura, D., Furuya, G., Ishikawa, S., 2023. Immune repertoire profiling for disease pathobiology. Pathology International 73, 1–11.
Mita, H., Katoh, H., Komura, D., Kakiuchi, M., Abe, H., Rokutan, H., Yagi, K., Nomura, S., Ushiku, T., Seto, Y., Ishikawa, S., 2022. Aberrant Cadherin11 Expression Predicts Distant Metastasis of Gastric Cancer. Pathology - Research and Practice 154294.
Matsubara, D., Yoshimoto, T., Akolekar, N., Totsuka, T., Amano, Y., Kihara, A., Miura, T., Isagawa, Y., Sakuma, Y., Ishikawa, S., Ushiku, T., Fukayama, M., Niki, T., 2022. Genetic and phenotypic determinants of morphologies in 3‐dimensional cultures and xenografts of lung tumor cell lines. Cancer Science cas.15702.
Furuya, G., Katoh, H., Atsumi, S., Hashimoto, I., Komura, D., Hatanaka, R., Senga, S., Hayashi, S., Akita, S., Matsumura, H., Miura, A., Mita, H., Nakakido, M., Nagatoishi, S., Sugiyama, A., Suzuki, R., Konishi, H., Yamamoto, A., Abe, H., Hiraoka, N., Aoki, K., Kato, Y., Seto, Y., Yoshimura, C., Miyadera, K., Tsumoto, K., Ushiku, T., Ishikawa, S., 2022. Nucleic acid–triggered tumoral immunity propagates pH ‐selective therapeutic antibodies through tumor‐driven epitope spreading. Cancer Science cas.15596.
Kaneko, Y., Yamatsugu, K., Yamashita, T., Takahashi, K., Tanaka, T., Aki, S., Tatsumi, T., Kawamura, T., Miura, M., Ishii, M., Ohkubo, K., Osawa, T., Kodama, T., Ishikawa, S., Tsukagoshi, M., Chansler, M., Sugiyama, A., Kanai, M., Katoh, H., 2022. Pathological complete remission of relapsed tumor by photo‐activating antibody–mimetic drug conjugate treatment. Cancer Science cas.15565.
Hongo, H., Miyawaki, S., Teranishi, Y., Mitsui, J., Katoh, H., Komura, D., Tsubota, K., Matsukawa, T., Watanabe, M., Kurita, M., Yoshimura, J., Dofuku, S., Ohara, K., Ishigami, D., Okano, A., Kato, M., Hakuno, F., Takahashi, A., Kunita, A., Ishiura, H., Shin, M., Nakatomi, H., Nagao, T., Goto, H., Takahashi, S.-I., Ushiku, T., Ishikawa, S., Okazaki, M., Morishita, S., Tsuji, S., Saito, N., 2022. Somatic GJA4 gain-of-function mutation in orbital cavernous venous malformations. Angiogenesis.
Tanaka, M., Kunita, A., Yamagishi, M., Katoh, H., Ishikawa, S., Yamamoto, H., Abe, J., Arita, J., Hasegawa, K., Shibata, T., Ushiku, T., 2022. KRAS mutation in intrahepatic cholangiocarcinoma: linkage with metastasis‐free survival and reduced E‐cadherin expression. Liver International liv.15366.
Liu, B., Katoh, H., Komura, D., Yamamoto, A., Ochi, M., Onoyama, T., Abe, H., Ushiku, T., Seto, Y., Suo, J., Ishikawa, S., 2022. Functional genomics screening identifies aspartyl‐ tRNA synthetase as a novel prognostic marker and a therapeutic target for gastric cancers. The Journal of Pathology path.5980.
Onoyama, T., Ishikawa, S., Isomoto, H., 2022. Gastric cancer and genomics: review of literature. J Gastroenterol.
Tsubosaka, A., Komura, D., Katoh, H., Kakiuchi, M., Onoyama, T., Yamamoto, A., Abe, H., Seto, Y., Ushiku, T., Ishikawa, S., 2022. Single-Cell Transcriptome Analyses Reveal the Cell Diversity and Developmental Features of Human Gastric and Metaplastic Mucosa. bioRxiv.
Teranishi, Y., Okano, A., Miyawaki, S., Ohara, K., Ishigami, D., Hongo, H., Dofuku, S., Takami, H., Mitsui, J., Ikemura, M., Komura, D., Katoh, H., Ushiku, T., Ishikawa, S., Shin, M., Nakatomi, H., Saito, N., 2022. Clinical significance of NF2 alteration in grade I meningiomas revisited; prognostic impact integrated with extent of resection, tumour location, and Ki-67 index. acta neuropathol commun 10, 76.
Komura, D., Onoyama, T., Shinbo, K., Odaka, H., Hayakawa, M., Ochi, M., Herdiantoputri, R., Sakamoto, K., Katoh, H., Ikeda, T., Ushiku, T., Ishikawa, S., 2022. Beyond pathologist-level annotation of large-scale cancer histology for semantic segmentation using immunofluorescence restaining. bioRxiv.
Yamatsugu, K., Katoh, H., Yamashita, T., Takahashi, K., Aki, S., Tatsumi, T., Kaneko, Y., Kawamura, T., Miura, M., Ishii, M., Ohkubo, K., Osawa, T., Kodama, T., Ishikawa, S., Kanai, M., Sugiyama, A., 2022. Antibody mimetic drug conjugate manufactured by high-yield Escherichia coli expression and non-covalent binding system. Protein Expression and Purification 192, 106043.
Yasuda, T., Lee, H.S., Nam, S.Y., Katoh, H., Ishibashi, Y., Yamagata Murayama, S., Matsui, H., Masuda, H., Rimbara, E., Sakurazawa, N., Suzuki, H., Yoshida, H., Seto, Y., Ishikawa, S., Jeon, S.W., Nakamura, M., Nomura, S., 2022. Non-Helicobacter pylori Helicobacter (NHPH) positive gastric cancer. Sci Rep 12, 4811.
Komura, D., Kawabe, A., Fukuta, K., Sano, K., Umezaki, T., Koda, H., Suzuki, R., Tominaga, K., Ochi, M., Konishi, H., Masakado, F., Saito, N., Sato, Y., Onoyama, T., Nishida, S., Furuya, G., Katoh, H., Yamashita, H., Kakimi, K., Seto, Y., Ushiku, T., Fukayama, M., Ishikawa, S., 2022. Universal encoding of pan-cancer histology by deep texture representations. Cell Reports 38, 110424.
Zhang, M., Sugita, I., Komura, D., Katoh, H., Shimada, S., Inazawa, J., Tanaka, S., Ishikawa, S., 2022. Genomic landscape of a mouse model of diffuse-type gastric adenocarcinoma. Gastric Cancer 25, 83–95.
Sugita, I., Matsuyama, S., Dobashi, H., Komura, D., Ishikawa, S., 2022. Viola: a structural variant signature extractor with user-defined classifications. Bioinformatics 38, 540–542.
Sueyoshi, K., Komura, D., Katoh, H., Yamamoto, A., Onoyama, T., Chijiwa, T., Isagawa, T., Tanaka, M., Suemizu, H., Nakamura, M., Miyagi, Y., Aburatani, H., Ishikawa, S., 2021. Multi-tumor analysis of cancer-stroma interactomes of patient-derived xenografts unveils the unique homeostatic process in renal cell carcinomas. iScience 24, 103322.
Ishigami, D., Miyawaki, S., Nakatomi, H., Takayanagi, S., Teranishi, Y., Ohara, K., Hongo, H., Dofuku, S., Kin, T., Abe, H., Mitsui, J., Komura, D., Katoh, H., Ishikawa, S., Saito, N., 2021. Brainstem intraparenchymal schwannoma with genetic analysis: a case report and literature review. BMC Med Genomics 14, 205.
Komura, D., Ishikawa, S., 2021. Advanced deep learning applications in diagnostic pathology. Translational and Regulatory Sciences 3, 36–42.
Katoh, H., Ishikawa, S., 2021. Lifestyles, genetics, and future perspectives on gastric cancer in east Asian populations. J Hum Genet 66, 887–899.
Imai, S., Ooki, T., Murata-Kamiya, N., Komura, D., Tahmina, K., Wu, W., Takahashi-Kanemitsu, A., Knight, C.T., Kunita, A., Suzuki, N., Del Valle, A.A., Tsuboi, M., Hata, M., Hayakawa, Y., Ohnishi, N., Ueda, K., Fukayama, M., Ushiku, T., Ishikawa, S., Hatakeyama, M., 2021. Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis. Cell Host Microbe 29, 941-958.e10.
Ohkuma, R., Yada, E., Ishikawa, S., Komura, D., Kubota, Y., Hamada, K., Horiike, A., Ishiguro, T., Hirasawa, Y., Ariizumi, H., Shida, M., Watanabe, M., Onoue, R., Ando, K., Tsurutani, J., Yoshimura, K., Sasada, T., Aoki, T., Murakami, M., Norose, T., Ohike, N., Takimoto, M., Kobayashi, S., Tsunoda, T., Wada, S., 2021. High levels of human epididymis protein 4 mRNA and protein expression are associated with chemoresistance and a poor prognosis in pancreatic cancer. Int J Oncol 58, 57–69.
Koyama, K., Maeda, D., Kito, M., Tamura, D., Kudo-Asabe, Y., Katoh, H., Ishikawa, S., Nanjo, H., Terada, Y., Goto, A., 2020. Clinicopathological and molecular analyses of linearly expanded epithelial cells with β-catenin alterations, “β-catenin signature”, in the normal fallopian tube. Histopathology 77, 880–889.
Atsumi, S., Katoh, H., Komura, D., Hashimoto, I., Furuya, G., Koda, H., Konishi, H., Suzuki, R., Yamamoto, A., Yuba, S., Abe, H., Rino, Y., Oshima, T., Ushiku, T., Fukayama, M., Seto, Y., Ishikawa, S., 2020. Focal adhesion ribonucleoprotein complex proteins are major humoral cancer antigens and targets in autoimmune diseases. Communications Biology 3, 1–15.
Shinozaki-Ushiku, A., Ishikawa, S., Komura, D., Seto, Y., Aburatani, H., Ushiku, T., 2020. The first case of gastric carcinoma with NTRK rearrangement: identification of a novel ATP1B-NTRK1 fusion. Gastric Cancer 23, 944–947.
Bailey, M.H., Meyerson, W.U., Dursi, L.J., Wang, L.-B., Dong, G., Liang, W.-W., Weerasinghe, A., Li, S., Kelso, S., MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena, G., Ellrott, K., Wendl, M.C., Wheeler, D.A., Getz, G., Simpson, J.T., Gerstein, M.B., Ding, L., PCAWG Consortium, 2020. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11, 4748.
Midorikawa, Y., Yamamoto, S., Tatsuno, K., Renard-Guillet, C., Tsuji, S., Hayashi, A., Ueda, H., Fukuda, S., Fujita, T., Katoh, H., Ishikawa, S., Covington, K.R., Creighton, C.J., Sugitani, M., Wheeler, D.A., Shibata, T., Nagae, G., Takayama, T., Aburatani, H., 2020. Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression. Cancer Res 80, 3810–3819.
Li, C.H., Prokopec, S.D., Sun, R.X., Yousif, F., Schmitz, N., PCAWG Tumour Subtypes and Clinical Translation, Boutros, P.C., PCAWG Consortium, 2020. Sex differences in oncogenic mutational processes. Nat Commun 11, 4330.
Ikeda, H., Muroi, M., Kondoh, Y., Ishikawa, S., Kakeya, H., Osada, H., Imoto, M., 2020. Miclxin, a Novel MIC60 Inhibitor, Induces Apoptosis via Mitochondrial Stress in β-Catenin Mutant Tumor Cells. ACS Chem Biol 15, 2195–2204.
Ohkuma, R., Yada, E., Ishikawa, S., Komura, D., Kubota, Y., Hamada, K., Horiike, A., Ishiguro, T., Hirasawa, Y., Ariizumi, H., Shida, M., Watanabe, M., Onoue, R., Ando, K., Tsurutani, J., Yoshimura, K., Sasada, T., Aoki, T., Murakami, M., Norose, T., Ohike, N., Takimoto, M., Kobayashi, S., Tsunoda, T., Wada, S., 2020. High expression levels of polymeric immunoglobulin receptor are correlated with chemoresistance and poor prognosis in pancreatic cancer. Oncol Rep 44, 252–262.
Komura, D., Kawabe, A., Fukuta, K., Sano, K., Umezaki, T., Koda, H., Suzuki, R., Tominaga, K., Konishi, H., Nishida, S., Furuya, G., Katoh, H., Ushiku, T., Fukayama, M., Ishikawa, S., 2020. Deep Texture Representations as a Universal Encoder for Pan-cancer Histology. bioRxiv 2020.07.28.224253.
Sano, K., Matsuda, S., Tohyama, S., Komura, D., Shimizu, E., Sutoh, C., 2020. Deep learning-based classification of the mouse estrous cycle stages. Scientific Reports 10, 11714.
Matsubara, D., Yoshimoto, T., Soda, M., Amano, Y., Kihara, A., Funaki, T., Ito, T., Sakuma, Y., Shibano, T., Endo, S., Hagiwara, K., Ishikawa, S., Fukayama, M., Murakami, Y., Mano, H., Niki, T., 2020. Reciprocal expression of trefoil factor-1 and thyroid transcription factor-1 in lung adenocarcinomas. Cancer Sci 111, 2183–2195.
Suzuki, A., Katoh, H., Komura, D., Kakiuchi, M., Tagashira, A., Yamamoto, S., Tatsuno, K., Ueda, H., Nagae, G., Fukuda, S., Umeda, T., Totoki, Y., Abe, H., Ushiku, T., Matsuura, T., Sakai, E., Ohshima, T., Nomura, S., Seto, Y., Shibata, T., Rino, Y., Nakajima, A., Fukayama, M., Ishikawa, S., Aburatani, H., 2020. Defined lifestyle and germline factors predispose Asian populations to gastric cancer. Science Advances 6, eaav9778.
Watabe, S., Kikuchi, Y., Morita, S., Komura, D., Numakura, S., Kumagai-Togashi, A., Watanabe, M., Matsutani, N., Kawamura, M., Yasuda, M., Uozaki, H., 2020. Clinicopathological significance of microRNA-21 in extracellular vesicles of pleural lavage fluid of lung adenocarcinoma and its functions inducing the mesothelial to mesenchymal transition. Cancer Med 9, 2879–2890.
Takai, E., Maeda, D., Li, Z., Kudo-Asabe, Y., Totoki, Y., Nakamura, H., Nakamura, A., Nakamura, R., Kirikawa, M., Ito, Y., Yoshida, M., Inoue, T., Habuchi, T., Ikoma, S., Katoh, H., Kato, M., Shibata, T., Ishikawa, S., Yachida, S., Goto, A., 2020. Post-mortem Plasma Cell-Free DNA Sequencing: Proof-of-Concept Study for the “Liquid Autopsy.” Scientific Reports 10, 1–10.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, 2020. Pan-cancer analysis of whole genomes. Nature 578, 82–93.
Hiroshima, Y., Kasajima, R., Kimura, Y., Komura, D., Ishikawa, S., Ichikawa, Y., Bouvet, M., Yamamoto, N., Oshima, T., Morinaga, S., Singh, S.R., Hoffman, R.M., Endo, I., Miyagi, Y., 2020. Novel targets identified by integrated cancer-stromal interactome analysis of pancreatic adenocarcinoma. Cancer Lett. 469, 217–227.
Ohkuma, R., Yada, E., Ishikawa, S., Komura, D., Ishizaki, H., Tamada, K., Kubota, Y., Hamada, K., Ishida, H., Hirasawa, Y., Ariizumi, H., Satoh, E., Shida, M., Watanabe, M., Onoue, R., Ando, K., Tsurutani, J., Yoshimura, K., Yokobori, T., Sasada, T., Aoki, T., Murakami, M., Norose, T., Ohike, N., Takimoto, M., Izumizaki, M., Kobayashi, S., Tsunoda, T., Wada, S., 2020. High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer. PLoS ONE 15, e0226707.
Akiyama, Y., Maeda, D., Katoh, H., Morikawa, T., Niimi, A., Nomiya, A., Sato, Y., Kawai, T., Goto, A., Fujimura, T., Fukuhara, H., Nakagawa, T., Igawa, Y., Ishikawa, S., Fukayama, M., Kume, H., Homma, Y., 2019. Molecular Taxonomy of Interstitial Cystitis/Bladder Pain Syndrome Based on Whole Transcriptome Profiling by Next-Generation RNA Sequencing of Bladder Mucosal Biopsies. J. Urol. 202, 290–300.
Nishizawa, T., Nakano, K., Fujii, E., Komura, D., Kuroiwa, Y., Ishimaru, C., Monnai, M., Aburatani, H., Ishikawa, S., Suzuki, M., 2019. In vivo effects of mutant RHOA on tumor formation in an orthotopic inoculation model. Oncology Reports 42, 1745–1754.
Suga, H., Oka, T., Sugaya, M., Sato, Y., Ishii, T., Nishida, H., Ishikawa, S., Fukayama, M., Sato, S., 2019. Keratinocyte Proline-Rich Protein Deficiency in Atopic Dermatitis Leads to Barrier Disruption. Journal of Investigative Dermatology 139, 1867-1875.e7.
Komura, D., Ishikawa, S., 2019. Machine learning approaches for pathologic diagnosis. Virchows Arch 475, 131–138.
Konishi, H., Komura, D., Katoh, H., Atsumi, S., Koda, H., Yamamoto, A., Seto, Y., Fukayama, M., Yamaguchi, R., Imoto, S., Ishikawa, S., 2019. Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. BMC Bioinformatics 20, 267.
Krishnan, N.M., Katoh, H., Palve, V., Pareek, M., Sato, R., Ishikawa, S., Panda, B., 2019. Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma. PeerJ 7, e6464.
Bándi, P., Geessink, O., Manson, Q., Van Dijk, M., Balkenhol, M., Hermsen, M., Ehteshami Bejnordi, B., Lee, B., Paeng, K., Zhong, A., Li, Q., Zanjani, F.G., Zinger, S., Fukuta, K., Komura, D., Ovtcharov, V., Cheng, S., Zeng, S., Thagaard, J., Dahl, A.B., Lin, H., Chen, H., Jacobsson, L., Hedlund, M., Çetin, M., Halıcı, E., Jackson, H., Chen, R., Both, F., Franke, J., Küsters-Vandevelde, H., Vreuls, W., Bult, P., van Ginneken, B., van der Laak, J., Litjens, G., 2019. From Detection of Individual Metastases to Classification of Lymph Node Status at the Patient Level: The CAMELYON17 Challenge. IEEE Transactions on Medical Imaging 38, 550–560.
Okamoto, H., Yoshimatsu, Y., Tomizawa, T., Kunita, A., Takayama, R., Morikawa, T., Komura, D., Takahashi, K., Oshima, T., Sato, M., Komai, M., Podyma-Inoue, K.A., Uchida, H., Hamada, H., Fujiu, K., Ishikawa, S., Fukayama, M., Fukuhara, T., Watabe, T., 2019. Interleukin-13 receptor α2 is a novel marker and potential therapeutic target for human melanoma. Scientific Reports 9, 1281.
Nakayama, A., Abe, H., Kunita, A., Saito, R., Kanda, T., Yamashita, H., Seto, Y., Ishikawa, S., Fukayama, M., 2019. Viral loads correlate with upregulation of PD-L1 and worse patient prognosis in Epstein–Barr Virus-associated gastric carcinoma. PLOS ONE 14, e0211358.
Komura, D., Ishikawa, S., 2018. Machine Learning Methods for Histopathological Image Analysis. Comput Struct Biotechnol J 16, 34–42.
Funahashi, S.-I., Kawai, S., Fujii, E., Taniguchi, K., Nakano, K., Ishikawa, S., Aburatani, H., Suzuki, M., 2018. Generation of an anti-desmoglein 3 antibody without pathogenic activity of pemphigus vulgaris for therapeutic application to squamous cell carcinoma. J. Biochem. 164, 471–481.
Nakano, K., Nishizawa, T., Komura, D., Fujii, E., Monnai, M., Kato, A., Funahashi, S.-I., Ishikawa, S., Suzuki, M., 2018. Difference in morphology and interactome profiles between orthotopic and subcutaneous gastric cancer xenograft models. J Toxicol Pathol 31, 293–300.
Hosonaga, M., Arima, Y., Sampetrean, O., Komura, D., Koya, I., Sasaki, T., Sato, E., Okano, H., Kudoh, J., Ishikawa, S., Saya, H., Ishikawa, T., 2018. HER2 Heterogeneity Is Associated with Poor Survival in HER2-Positive Breast Cancer. Int J Mol Sci 19.
Tanaka, A., Ishikawa, S., Ushiku, T., Yamazawa, S., Katoh, H., Hayashi, A., Kunita, A., Fukayama, M., 2018. Frequent CLDN18-ARHGAP fusion in highly metastatic diffuse-type gastric cancer with relatively early onset. Oncotarget 9, 29336–29350.
Wang, C.-W., Lee, Y.-C., Calista, E., Zhou, F., Zhu, H., Suzuki, R., Komura, D., Ishikawa, S., Cheng, S.-P., 2018. A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays. Bioinformatics 34, 1767–1773.
Nishizawa, T., Nakano, K., Harada, A., Kakiuchi, M., Funahashi, S.-I., Suzuki, M., Ishikawa, S., Aburatani, H., 2018. DGC-specific RHOA mutations maintained cancer cell survival and promoted cell migration via ROCK inactivation. Oncotarget 9, 23198–23207.
